Mechanism of persister formation in response to nitrogen starvation

Bacterial resistance to antibiotics is a major problem, but most chronic infections that are recalcitrant to therapy are caused by drug-susceptible pathogens. This paradox is explained by the presence of a small population of quiescent persister cells that are tolerant of killing by antibiotics. Persisters typically have a decreased level of ATP, and diminished activity of antibiotic targets. This leads to persister tolerance of antibiotics that kill by corrupting their targets. We reasoned that starvation for nutrients that do not affect the energy level may represent an additional general mechanism of persister formation. In a culture of E. coli experiencing nitrogen starvation, persister levels sharply rise without a change in ATP. Here we show that PyrBI, a key enzyme in nitrogen assimilation and de novo nucleotide synthesis, is largely responsible for persister formation under nitrogen-limiting conditions. Tracking individual cells in a mother machine shows that persisters have low levels of PyrBI. Similarly, PyrBI is low in persisters present in a biofilm. Overexpression of PyrBI quenches the noise in its expression, decreasing persistence. Starvation for other essential nutrients could similarly induce persistence, with stochastic fluctuation in persister gene expression serving as a general mechanism of persister formation. Populations of antibiotic-susceptible bacteria can include some quiescent persister cells that are tolerant of killing by the drugs and often have low ATP levels. Here, Taher et al. show that nitrogen starvation drives persister formation through stochastic downregulation of pyrimidine synthesis, reducing drug target activity without ATP depletion.